Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping

Abstract

Summary: Many drug or single nucleotide polymorphism (SNP)-related resources and tools have been developed, but connecting and integrating them is still a challenge. Here, we describe a user-friendly web-based software package, named Drug-SNPing, which provides a platform for the integration of drug information (DrugBank and PharmGKB), protein–protein interactions (STRING), tagSNP selection (HapMap) and genotyping information (dbSNP, REBASE and SNP500Cancer). DrugBank-based inputs include the following: (i) common name of the drug, (ii) synonym or drug brand name, (iii) gene name (HUGO) and (iv) keywords. PharmGKB-based inputs include the following: (i) gene name (HUGO), (ii) drug name and (iii) disease-related keywords. The output provides drug-related information, metabolizing enzymes and drug targets, as well as protein–protein interaction data. Importantly, tagSNPs of the selected genes are retrieved for genotyping analyses. All drug-based and protein–protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes. Thus, users can enter any drug keywords/brand names to obtain immediate information that is highly relevant to genotyping for pharmacogenomics research. Availability and implementation: Drug-SNPing and its user manual are freely available at http://bio.kuas.edu.tw/drug-snping/. Contact: chuang@isu.edu.tw; yuhuei.cheng@gmail.com; changhw@kmu.edu.tw

SNP 1772 C > T of HIF-1α gene associates with breast cancer risk in a Taiwanese population

“…PCR was performed with the following protocol: 94°C (1 min); 4 cycles of 94°C (15 s), 64°C (15 s), 70°C (8 s); 4 cycles of 94°C (15 s), 61°C (15 s), 70°C (8 s); 4 cycles of 94°C (15 s), 58°C (15 s), 70°C (8 s); 60 cycles of 94°C for (15 s), 55°C (15 s), 70°C (8 s); 94°C (1 min) and 60°C (5 min). The available restriction enzyme for HIF-1α 1772 C > T (rs11549465) was retrieved from the SNP-RFLP freeware [ 29 - 31 ]. PCR products were digested with the Hph I restriction enzyme (NEB) at 37°C for overnight and then they were subjected to 3% agarose electrophoresis and stained with SYBR Safe™ DNA gel stain (Invitrogen) for visualization of the PCR-restriction fragment length polymorphism (PCR-RFLP) patterns.…”

Structural designing of suppressors for autisms spectrum diseases using molecular dynamics sketch

“…[11] A technique to infer protein-chemical interactionsusing heterogeneous input consisting of both protein sequenceand chemical information. [12] user-friendly web-based software, named Drug-SN Ping, which provides a platform for the integration of drug information. [13] Several variant genotypes along with the development of Quasi-species restricted the effectiveness of drugs used for the treatment of HCV infections.…”

Breast cancer-associated high-order SNP-SNP interaction of CXCL12/CXCR4-related genes by an improved multifactor dimensionality reduction (MDR-ER)

“…The effective identification and screening of biomarkers for breast cancer prediction may reduce the occurrence of breast cancer (1). Single nucleotide polymorphisms (SNPs), the most abundant variants of the human genome (2), have become significant biomarkers for personalized medicine and the recognition of disease/cancer susceptibility (3)(4)(5).…”